bug with merging?

[Cammer, Michael]

We have two stacks of grayscale images we want to merge.  If we put them in the R G or B channels, the entire stacks merge fine.  However, if we put one of the stacks in the gray channel, only the first slice of the stacks is merged (see http://www.flickr.com/photos/mcammer/7980179925/ ).
Is this a bug or is there something else we need to do?
Thanks!

________________________________________________________
Michael Cammer, Assistant Research Scientist
Skirball Institute of Biomolecular Medicine
Lab: [phone]  Cell: [phone]


--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Glen MacDonald-2]

Try selecting 'Create composite'.  I've been merging 3 to 7 channels, with 1 as gray, without issue.  If RGB is needed then convert. The gray channel will be merged into the RGB channels, so keep the composite for future channel editing.  

Glen
Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center
Box 357923
University of Washington
Seattle, WA 98195-7923  USA
[phone]
[hidden email]








On Sep 12, 2012, at 11:17 AM, Cammer, Michael wrote:

> We have two stacks of grayscale images we want to merge.  If we put them in the R G or B channels, the entire stacks merge fine.  However, if we put one of the stacks in the gray channel, only the first slice of the stacks is merged (see http://www.flickr.com/photos/mcammer/7980179925/ ).
> Is this a bug or is there something else we need to do?
> Thanks!
>
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist
> Skirball Institute of Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Cammer, Michael]

Thanks.
We'll stick with composite for now (RAM and disk space are cheap) and it has the benefit of keeping the raw data.
Regards,
Michael

-----Original Message-----
From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Glen MacDonald
Sent: Wednesday, September 12, 2012 3:16 PM
To: [hidden email]
Subject: Re: bug with merging?

Try selecting 'Create composite'.  I've been merging 3 to 7 channels, with 1 as gray, without issue.  If RGB is needed then convert. The gray channel will be merged into the RGB channels, so keep the composite for future channel editing.  

Glen
Glen MacDonald
Core for Communication Research
Virginia Merrill Bloedel Hearing Research Center Box 357923 University of Washington Seattle, WA 98195-7923  USA
[phone]
[hidden email]








On Sep 12, 2012, at 11:17 AM, Cammer, Michael wrote:

> We have two stacks of grayscale images we want to merge.  If we put them in the R G or B channels, the entire stacks merge fine.  However, if we put one of the stacks in the gray channel, only the first slice of the stacks is merged (see http://www.flickr.com/photos/mcammer/7980179925/ ).
> Is this a bug or is there something else we need to do?
> Thanks!
>
> ________________________________________________________
> Michael Cammer, Assistant Research Scientist Skirball Institute of
> Biomolecular Medicine
> Lab: [phone]  Cell: [phone]
>
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html

[Michael P Ellis]

Michael, we work a lot with stacks and I was not able to reproduce your problem.

This little script create 4 8 bit grey scale stacks and then merges them. It seems to work fine

run("Hyperstack...", "title=Red type=8-bit display=Composite width=300 height=200 channels=1 slices=1 frames=5 label");
run("Hyperstack...", "title=Green type=8-bit display=Composite width=300 height=200 channels=1 slices=1 frames=5 label");
run("Hyperstack...", "title=Blue type=8-bit display=Composite width=300 height=200 channels=1 slices=1 frames=5 label");
run("Hyperstack...", "title=Grey type=8-bit display=Composite width=300 height=200 channels=1 slices=1 frames=5 label");
run("Merge Channels...", "c1=Red c2=Green c3=Blue c4=Grey create");

(Running Image 1.47c on Mac OS 10.6)

You also might like our Composite Adjuster plugin. It's an interactive tool for adjusting the colours, brightness and contrast, for multi dimensional composite images. You can pick it up from here:

http://www.dsuk.biz/DSUK/SmartCaptureLite.html

There is a YouTube movie that gives you 20 quick overview of it's main features here:
http://www.youtube.com/embed/g0hoRLxBlWE?rel=0&hd=1

-- Michael Ellis

On 12 Sep 2012, at 21:36, Cammer, Michael wrote:

> Thanks.
> We'll stick with composite for now (RAM and disk space are cheap) and it has the benefit of keeping the raw data.
> Regards,
> Michael
>
> -----Original Message-----
> From: ImageJ Interest Group [mailto:[hidden email]] On Behalf Of Glen MacDonald
> Sent: Wednesday, September 12, 2012 3:16 PM
> To: [hidden email]
> Subject: Re: bug with merging?
>
> Try selecting 'Create composite'.  I've been merging 3 to 7 channels, with 1 as gray, without issue.  If RGB is needed then convert. The gray channel will be merged into the RGB channels, so keep the composite for future channel editing.  
>
> Glen
> Glen MacDonald
> Core for Communication Research
> Virginia Merrill Bloedel Hearing Research Center Box 357923 University of Washington Seattle, WA 98195-7923  USA
> [phone]
> [hidden email]
>
>
>
>
>
>
>
>
> On Sep 12, 2012, at 11:17 AM, Cammer, Michael wrote:
>
>> We have two stacks of grayscale images we want to merge.  If we put them in the R G or B channels, the entire stacks merge fine.  However, if we put one of the stacks in the gray channel, only the first slice of the stacks is merged (see http://www.flickr.com/photos/mcammer/7980179925/ ).
>> Is this a bug or is there something else we need to do?
>> Thanks!
>>
>> ________________________________________________________
>> Michael Cammer, Assistant Research Scientist Skirball Institute of
>> Biomolecular Medicine
>> Lab: [phone]  Cell: [phone]
>>
>>
>> --
>> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html
>
> --
> ImageJ mailing list: http://imagej.nih.gov/ij/list.html

--
ImageJ mailing list: http://imagej.nih.gov/ij/list.html